Biocview "SNP"

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

A Genetic-Based Assay for the Identification of Cell Lines

A Genotype Calling Algorithm for Affymetrix SNP Arrays

Analysis of Large Affymetrix Microarray Data Sets

Analysis of Parent-Specific DNA Copy Numbers

Analytical Tools for MassArray Data

Ancestry Specific Allele Frequency Estimation

Annotation of Genetic Variants

An R package for analysis of case-control studies in genetic epidemiology

An R package for computing the number of susceptibility SNPs

An R package to identify multi-snp effects in nuclear family studies using the GADGETS method

A Package for De Novo CNV Detection in Case-Parent Trios

A package for variant peptides detection and visualization in shotgun proteomics.

appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV

A RangedSummarizedExperiment with methods for copy number analysis

Asessing statistical significance in predictive GWA studies

Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

Bayesian analysis of Gaussian GWAS data

Bayesian Piecewise Constant Regression for DNA copy number estimation

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

Bioconductor components for general cancer genomics

Candidate Gene Miner

Candidate gene prioritization based on convergent evidence

Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

Comprehensive QTL annotation of GWAS results

Copy-Number Analysis of Large Microarray Data Sets

data structures for linkage disequilibrium measures in populations

Decomposition of individual tumors into mutational signatures by signature refitting

Detection, Characterization and Visualization of Kataegis in Sequencing Data

Detection of site fixation in molecular evolution

Detection of subclonal SNVs in deep sequencing data.

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Dual redundant reference sequencing

Error correction tool for noisy genotyping by sequencing (GBS) data

Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Filtering of coding and non-coding genetic variants

Find SNV/Indel differences between two bam files with near relationship

GEM: fast association study for the interplay of Gene, Environment and Methylation

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Generate customized protein databases from NGS data for proteomics search

Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

GeneRegionScan

genesis assocation testing code rewrite

Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

Genomic Knowledge-guided Multiple Testing

Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

Genotype Conditional Association TEST

Genotype Imputed Gene Set Enrichment Analysis

Genotyping and QTL Mapping in DO Mice

Get inversion status in predefined regions

Get the QTL/gene/SNP data functions

Gimpute: An efficient genetic data processing and imputation pipeline

gin in R

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

gQTLBase: infrastructure for eQTL, mQTL and similar studies

gQTLstats: computationally efficient analysis for eQTL and allied studies

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

GWAS-based Mendelian Randomization and Path Analyses

GWAS for Selfing Species

GWAS Incorporating Networks

gwasurvivr: an R package for genome wide survival analysis

hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

Hierarchical Inference

High-Throughput Sequence Analysis using the Aroma Framework

iASeq: integrating multiple sequencing datasets for detecting allele-specific events

Identification of candidate genes associated with genetic variation

Identification of genetic Variants affecting Alternative Splicing

Identification of SNP Interactions

Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells

Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells

Infrastructure for Biostrings-based genome data packages

In-silico methods for genetic finemapping in inbred mice

integrated Bayesian Modeling of eQTL data

Integrated Copy Number Variation detection

Integrating Multi-Omic Network Data With Summay-Level GWAS Data

Integrative analysis of Multi-omics data for Alternative Splicing

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Integrative Statistics of alleLe Dependent Expression

Inversions in genotype data

Iterative Pruning to Capture Population Structure

Iterative Pruning to Capture Population Structure version 2

Logistic Factor Analysis for Categorical Data

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

Mapping, quantification and variant analysis of sequencing data

Mean Alterations Using Discrete Expression

Metabolomic Quantitative Trait Locus Mapping for 1H NMR data

Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Normalization and reporting of Illumina SNP bead arrays

Objective Assessment of Copy-Number Estimates

Optimal p-value weighting with independent information

Parallel implmentation of bounded memory GEE

Perform Chromosomal Ancestry Differences (CAnD) Analyses

Phylogeny-based sequence clustering with site polymorphism

Post-normalization of total copy numbers

Preprocessing tools for oligonucleotide arrays

Preprocessing tools for oligonucleotide arrays.

Processing Various Types of Data on GEO and TCGA

QA/QC of a gVCF or VCF file

Query data from SNPedia

Representation and manipulation of short genomic alignments

'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

R Interface to Ensembl Variant Effect Predictor

R Interface with InterMine-Powered Databases

R package for RIVER (RNA-Informed Variant Effect on Regulation)

Segmentation of single- and multi-track copy number data by penalized least squares regression.

Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

Semi-Supervised Mixture Model

Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

SnpMatrix and XSnpMatrix classes and methods

software and data for analyses in genetics of gene expression

Software infrastructure for efficient representation of full genomes and their SNPs

Standardise summary statistics from GWAS

Summarization and expression/phenotype association of CNV ranges

Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: workflow management and report generation environment

Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

The data package associated with the MAGAR R-package

The 'snp.matrix' and 'X.snp.matrix' Classes

The subREgion-based BurdEn Test (REBET)

Tools for building SNPlocs data packages

Tools for Genome Wide Association Studies

Tools for Sanger Sequencing Data in R

Tools for Testing Gene-Gene Interaction at the Gene Level

Tools for variant data

Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation

Visual comparison of mutational processes in a set of tumors

Visualizations for copy number alterations

visualize genome-wide association study with gene annotation and linkage disequiblism

Biocview "SNP"

R Package Documentation

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